Elena, yes it's in the test directory:
[mccssmb2@redqueen hdf5-1.8.7]$ ls -alt test/th5s*
-rw-r--r-- 1 mccssmb2 users 253104 Jun 25 11:29 test/th5s.o
-rw-r--r-- 1 mccssmb2 users 86268 Apr 22 21:52 test/th5s.c
-rw-r--r-- 1 mccssmb2 users 2049 Apr 20 22:22 test/th5s.h5
[mccssmb2@redqueen hdf5-1.8.7]$
Thanks, Michael
On 25 Jun 2011, at 12:07, Elena Pourmal wrote:
>
> Could you please check that th5s.h5 is indeed in the test directory?
> On Jun 25, 2011, at 2:35 PM, Michael Bane wrote:
>
>> Editting config/intel-flags then a fresh ./configure sorted that, thanks.
>> Done a
>> make clean && make -j 12 && make test
>> but still see the problem...
>>
>> Ta, M
>> <config.log>
>> On 25 Jun 2011, at 11:13, Elena Pourmal wrote:
>>
>>> Michael,
>>>
>>> Then you have to modify intel-flags file (or did you already ?)
>>>
>>> Elena
>>> On Jun 25, 2011, at 1:30 PM, Michael Bane wrote:
>>>
>>>> I've tried setting CC as you said but at 'make' stage it's being ignored
>>>> it seems:
>>>>
>>>> [mccssmb2@redqueen hdf5-1.8.7]$ make
>>>> Making all in src
>>>> make[1]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
>>>> make all-am
>>>> make[2]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
>>>> CC H5.lo
>>>> icc: command line warning #10120: overriding '-O2' with '-O3'
>>>> H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
>>>> H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
>>>> CC H5checksum.lo
>>>> icc: command line warning #10120: overriding '-O2' with '-O3'
>>>> CC H5dbg.lo
>>>> icc: command line warning #10120: overriding '-O2' with '-O3'
>>>>
>>>>
>>>> On 24 Jun 2011, at 19:43, Elena Pourmal wrote:
>>>>
>>>>> Michael,
>>>>>
>>>>> In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the
>>>>> higher level of optimization doesn't work on your machine (errors sound
>>>>> familiar, but I may be wrong)
>>>>>
>>>>> Could you please set CC to "icc -O2" and recompile the library, or fix
>>>>> the config/intel-flags file (search 1.8.7 string to find the right place).
>>>>>
>>>>> Thank you!
>>>>>
>>>>> Elena
>>>>> On Jun 24, 2011, at 4:01 PM, michael bane wrote:
>>>>>
>>>>>> My hdf5 1.8.7 appears to build okay but my make check fails. This is on
>>>>>> a Sci Linux box:
>>>>>> uname -a
>>>>>> Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18
>>>>>> 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
>>>>>>
>>>>>> I attach the std out+err from my configure and make steps. And here is
>>>>>> the detailed error
>>>>>>
>>>>>> [mccssmb2@redqueen hdf5-1.8.7]$
>>>>>> /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select
>>>>>> 2>&1 | less
>>>>>>
>>>>>> For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5
>>>>>> -help
>>>>>> Linked with hdf5 version 1.8 release 7
>>>>>> Testing -- Configure definitions (config)
>>>>>> Testing -- Encoding/decoding metadata (metadata)
>>>>>> Testing -- Checksum algorithm (checksum)
>>>>>> Testing -- Ternary Search Trees (tst)
>>>>>> Testing -- Memory Heaps (heap)
>>>>>> Testing -- Skip Lists (skiplist)
>>>>>> Testing -- Reference Counted Strings (refstr)
>>>>>> Testing -- Low-Level File I/O (file)
>>>>>> Testing -- Generic Object Functions (objects)
>>>>>> Testing -- Dataspaces (h5s)
>>>>>> *** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
>>>>>> HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
>>>>>> #000: H5F.c line 1522 in H5Fopen(): unable to open file
>>>>>> major: File accessability
>>>>>> minor: Unable to open file
>>>>>> #001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun
>>>>>> 24 12:41:23 2011
>>>>>> , name = 'th5s.h5', tent_flags = 0
>>>>>> major: File accessability
>>>>>> minor: Unable to open file
>>>>>> #002: H5FD.c line 1086 in H5FD_open(): open failed
>>>>>> major: Virtual File Layer
>>>>>> minor: Unable to initialize object
>>>>>> #003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name
>>>>>> = 'th5s.h5', errno = 2, error mess
>>>>>> age = 'No such file or directory', flags = 0, o_flags = 0
>>>>>> major: File accessability
>>>>>> minor: Unable to open file
>>>>>> ***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
>>>>>> Testing -- Dataspace coordinates (coords)
>>>>>> Testing -- Shared Object Header Messages (sohm)
>>>>>> Testing -- Attributes (attr)
>>>>>> Testing -- Selections (select)
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> large cube written from small cube has bad data! Line=2256
>>>>>> large cube written from small cube has bad data! Line=2256
>>>>>> large cube written from small cube has bad data! Line=2256
>>>>>> large cube written from small cube has bad data! Line=2256
>>>>>> large cube written from small cube has bad data! Line=2256
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> large cube read from small cube has bad data! Line=2015
>>>>>> {& much more of same}
>>>>>>
>>>>>>
>>>>>> Many thanks, Michael
>>>>>> <mkb_make.txt><mkb_configure.txt>_______________________________________________
>>>>>> Hdf-forum is for HDF software users discussion.
>>>>>> [email protected]
>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Hdf-forum is for HDF software users discussion.
>>>>> [email protected]
>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>>
>>>>
>>>> _______________________________________________
>>>> Hdf-forum is for HDF software users discussion.
>>>> [email protected]
>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>>
>>>
>>> _______________________________________________
>>> Hdf-forum is for HDF software users discussion.
>>> [email protected]
>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> [email protected]
>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
